Kinetics from Implicit Solvent Simulations of Biomolecules as a Function of Viscosity.

Kinetic properties of alanine dipeptide, the B1 domain of streptococcal protein G, and ubiquitin are compared between explicit solvent and implicit solvent simulations with the generalized Born molecular volume (GBMV) method. The results indicate that kinetics from explicit solvent simulations and experiments can be matched closely when the implicit solvent simulations are combined with Langevin dynamics and a friction coefficient near 10 ps(-1). Smaller and larger friction coefficients accelerate and slow down conformational sampling. It is found that local conformational exploration without the crossing of significant barriers can be accelerated by a factor of 4-5; however, the acceleration of barrier crossings is limited to about a factor of 2. The use of a Nosé-Hoover thermostat instead of Langevin dynamics greatly enhances local conformational sampling but slows down the crossing of barriers by at least an order of magnitude because of the lack of solute-solvent stochastic collisions.